MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
You know, when I was designing this, I thought of adding an option to select the number of fastener hole columns, so that one could configure a single column of fastener holes on each leaf, like a piano hinge. I'll see if I can add the option. Should be doable.
In the meantime, something you could do to line up the holes exactly, is to compute the hinge width as follows.
hinge_width = 4 x fastener_margin + 2 x fastener_head_diameter + 2 x leaf_gauge
This will align all the fastener holes on each leaf into a single column. Even if you specify an even number of holes for each leaf, they will overlap exactly to form single holes with that formula.